Cruises donot come to the bordertowns, in general they are about 1000 mile away from Mazatlan, P. Vallarta etc. on the Mexican Riviera.
Yes some ships come to Acapulco, but remember those problems are all drugs-related.
Cabo, Mazatlan, Puerto vallarta are all fine and safe.
But as always use your common-sense, which you also do in cities in the USA, Canada and Europe.